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PIO standalone capability and IO testing additions #447

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merged 9 commits into from
May 22, 2020
Merged

PIO standalone capability and IO testing additions #447

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9b8ec80
add pio standalone capability on cheyenne, add cheyenne_gnu, cheyenne…
apcraig May 17, 2020
394603d
add history_format, add support for pio1.10.1 and pio2.4.2 testing on…
apcraig May 18, 2020
7a4643e
clean up restart_format
apcraig May 18, 2020
8fe9e3c
fix bug in drivers/mct/cesm1/CICE_RunMod.F90 and update documentation
apcraig May 18, 2020
5431560
rebase to current master, fix a couple of minor precision8 bugs, upda…
apcraig May 20, 2020
a900320
add set_nml.cdf64
apcraig May 20, 2020
26bff18
fix error in mct/cesm1 code
apcraig May 21, 2020
6cb30e7
fix nfsd default value and remove io_pio
apcraig May 22, 2020
17160ad
update documentation and add nfsd error check
apcraig May 22, 2020
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20 changes: 9 additions & 11 deletions cicecore/cicedynB/analysis/ice_history.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -30,10 +30,11 @@
module ice_history

use ice_kinds_mod
use ice_communicate, only: my_task, master_task
use ice_constants, only: c0, c1, c2, c100, c360, c180, &
p001, p25, p5, mps_to_cmpdy, kg_to_g, spval
use ice_fileunits, only: nu_nml, nml_filename, nu_diag, &
get_fileunit, release_fileunit
get_fileunit, release_fileunit, flush_fileunit
use ice_exit, only: abort_ice
use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted
use icepack_intfc, only: icepack_snow_temperature, icepack_ice_temperature
Expand Down Expand Up @@ -62,7 +63,6 @@ subroutine init_hist (dt)

use ice_blocks, only: nx_block, ny_block
use ice_broadcast, only: broadcast_scalar, broadcast_array
use ice_communicate, only: my_task, master_task
use ice_calendar, only: yday, days_per_year, histfreq, &
histfreq_n, nstreams
use ice_domain_size, only: max_blocks, max_nstrm, nilyr, nslyr, nblyr, ncat, nfsd
Expand Down Expand Up @@ -1570,10 +1570,6 @@ subroutine init_hist (dt)
if (allocated(Tsnz4d)) deallocate(Tsnz4d)
allocate(Tsnz4d(nx_block,ny_block,nzslyr,ncat_hist))
endif
if (f_Sinz (1:1) /= 'x') then
if (allocated(Sinz4d)) deallocate(Sinz4d)
allocate(Sinz4d(nx_block,ny_block,nzilyr,ncat_hist))
endif

!-----------------------------------------------------------------
! 4D (floe size, thickness categories) variables looped separately
Expand Down Expand Up @@ -1616,6 +1612,8 @@ subroutine init_hist (dt)
ntmp(:) = 0
if (my_task == master_task) then
write(nu_diag,*) ' '
write(nu_diag,*) 'total number of history fields = ',num_avail_hist_fields_tot
write(nu_diag,*) 'max number of history fields = ',max_avail_hist_fields
write(nu_diag,*) 'The following variables will be ', &
'written to the history tape: '
write(nu_diag,101) 'description','units','variable','frequency','x'
Expand Down Expand Up @@ -1687,7 +1685,7 @@ subroutine init_hist (dt)
if (allocated(a3Df)) a3Df(:,:,:,:,:) = c0
if (allocated(a4Di)) a4Di(:,:,:,:,:,:) = c0
if (allocated(a4Ds)) a4Ds(:,:,:,:,:,:) = c0
if (allocated(a4Ds)) a4Df(:,:,:,:,:,:) = c0
if (allocated(a4Df)) a4Df(:,:,:,:,:,:) = c0
avgct(:) = c0
albcnt(:,:,:,:) = c0

Expand Down Expand Up @@ -2970,7 +2968,7 @@ subroutine accum_hist (dt)
enddo
enddo
enddo
call accum_hist_field(n_Tinz-n3Dacum, iblk, nzilyr, ncat_hist, &
call accum_hist_field(n_Tinz-n3Dfcum, iblk, nzilyr, ncat_hist, &
Tinz4d(:,:,1:nzilyr,1:ncat_hist), a4Di)
endif
if (f_Sinz (1:1) /= 'x') then
Expand All @@ -2984,7 +2982,7 @@ subroutine accum_hist (dt)
enddo
enddo
enddo
call accum_hist_field(n_Sinz-n3Dacum, iblk, nzilyr, ncat_hist, &
call accum_hist_field(n_Sinz-n3Dfcum, iblk, nzilyr, ncat_hist, &
Sinz4d(:,:,1:nzilyr,1:ncat_hist), a4Di)
endif

Expand Down Expand Up @@ -3796,7 +3794,7 @@ subroutine accum_hist (dt)
enddo ! n

do n = 1, num_avail_hist_fields_4Di
nn = n3Dacum + n
nn = n3Dfcum + n
if (avail_hist_fields(nn)%vhistfreq == histfreq(ns)) then
do k = 1, nzilyr
do ic = 1, ncat_hist
Expand Down Expand Up @@ -4025,7 +4023,7 @@ subroutine accum_hist (dt)
if (avail_hist_fields(n)%vhistfreq == histfreq(ns)) a3Df(:,:,:,nn,:) = c0
enddo
do n = n3Dfcum + 1, n4Dicum
nn = n - n3Dacum
nn = n - n3Dfcum
if (avail_hist_fields(n)%vhistfreq == histfreq(ns)) a4Di(:,:,:,:,nn,:) = c0
enddo
do n = n4Dicum + 1, n4Dscum
Expand Down
22 changes: 9 additions & 13 deletions cicecore/cicedynB/analysis/ice_history_fsd.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -428,11 +428,6 @@ subroutine accum_hist_fsd (iblk)
call accum_hist_field(n_fsdperim, iblk, worka, a2D)
endif






endif ! a2D allocated

! 3D category fields
Expand Down Expand Up @@ -474,19 +469,20 @@ subroutine accum_hist_fsd (iblk)
if (allocated(a4Df)) then

if (f_afsdn(1:1) /= 'x') then
do n = 1, ncat_hist
do k = 1, nfsd_hist
do j = 1, ny_block
do i = 1, nx_block
do n = 1, ncat_hist
do k = 1, nfsd_hist
workd(i,j,k,n) = trcrn(i,j,nt_fsd+k-1,n,iblk) &
* aicen_init(i,j,n,iblk)/floe_binwidth(k)
end do
end do
workd(i,j,k,n) = trcrn(i,j,nt_fsd+k-1,n,iblk) &
* aicen_init(i,j,n,iblk)/floe_binwidth(k)
end do
end do
end do
call accum_hist_field(n_afsdn-n4Dscum, iblk, &
nfsd_hist, ncat_hist, workd, a4Df)
end do
call accum_hist_field(n_afsdn-n4Dscum, iblk, nfsd_hist, ncat_hist, &
workd(:,:,1:nfsd_hist,1:ncat_hist), a4Df)
endif

endif ! a4Df allocated

endif ! tr_fsd
Expand Down
27 changes: 20 additions & 7 deletions cicecore/cicedynB/analysis/ice_history_shared.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,10 @@
module ice_history_shared

use ice_kinds_mod
use ice_communicate, only: my_task, master_task
use ice_domain_size, only: max_nstrm
use ice_exit, only: abort_ice
use ice_fileunits, only: nu_diag
use icepack_intfc, only: icepack_warnings_flush, icepack_warnings_aborted

implicit none
Expand All @@ -52,6 +54,9 @@ module ice_history_shared
character (len=char_len), public :: &
version_name

character (len=char_len), public :: &
history_format

!---------------------------------------------------------------
! Instructions for adding a field: (search for 'example')
! Here:
Expand Down Expand Up @@ -79,7 +84,7 @@ module ice_history_shared
end type

integer (kind=int_kind), parameter, public :: &
max_avail_hist_fields = 600 ! Max number of history fields
max_avail_hist_fields = 800 ! Max number of history fields

integer (kind=int_kind), public :: &
num_avail_hist_fields_tot = 0, & ! Current, total number of defined fields
Expand Down Expand Up @@ -111,8 +116,8 @@ module ice_history_shared
nzblyr , & ! bio grid
nzalyr ! aerosols (2 snow & nblyr+2 bio)

type (ice_hist_field), dimension(max_avail_hist_fields), public :: &
avail_hist_fields
type (ice_hist_field), public :: &
avail_hist_fields(max_avail_hist_fields)

integer (kind=int_kind), parameter, public :: &
nvar = 12 , & ! number of grid fields that can be written
Expand Down Expand Up @@ -806,8 +811,13 @@ subroutine define_hist_field(id, vname, vunit, vcoord, vcellmeas, &
num_avail_hist_fields_4Df = num_avail_hist_fields_4Df + 1
endif

if (num_avail_hist_fields_tot > max_avail_hist_fields) &
call abort_ice(subname//'ERROR: Need to increase max_avail_hist_fields')
if (num_avail_hist_fields_tot > max_avail_hist_fields) then
if (my_task == master_task) then
write(nu_diag,*) subname,' num_avail_hist_fields_tot = ',num_avail_hist_fields_tot
write(nu_diag,*) subname,' max_avail_hist_fields = ',max_avail_hist_fields
endif
call abort_ice(subname//'ERROR: Need in computation of max_avail_hist_fields')
endif

if (num_avail_hist_fields_tot /= &
num_avail_hist_fields_2D + &
Expand All @@ -819,8 +829,11 @@ subroutine define_hist_field(id, vname, vunit, vcoord, vcellmeas, &
num_avail_hist_fields_4Di + &
num_avail_hist_fields_4Ds + &
num_avail_hist_fields_4Df) then
call abort_ice(subname//'ERROR: num_avail_hist_fields error')
endif
if (my_task == master_task) then
write(nu_diag,*) subname,' num_avail_hist_fields_tot = ',num_avail_hist_fields_tot
endif
call abort_ice(subname//'ERROR: in num_avail_hist_fields')
endif

id(ns) = num_avail_hist_fields_tot

Expand Down
3 changes: 1 addition & 2 deletions cicecore/cicedynB/dynamics/ice_dyn_eap.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -2144,7 +2144,6 @@ subroutine read_restart_eap()
use ice_domain, only: nblocks, halo_info
use ice_grid, only: grid_type
use ice_restart, only: read_restart_field
use ice_restart_shared, only: restart_format

! local variables

Expand Down Expand Up @@ -2183,7 +2182,7 @@ subroutine read_restart_eap()
call read_restart_field(nu_restart_eap,0,a12_4,'ruf8', &
'a12_4',1,diag,field_loc_center,field_type_scalar) ! a12_4

if (trim(grid_type) == 'tripole' .and. trim(restart_format) == 'pio') then
if (trim(grid_type) == 'tripole') then

call ice_HaloUpdate_stress(a11_1, a11_3, halo_info, &
field_loc_center, field_type_scalar)
Expand Down
42 changes: 22 additions & 20 deletions cicecore/cicedynB/dynamics/ice_transport_driver.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -147,68 +147,70 @@ subroutine init_transport

! diagnostic output
if (my_task == master_task) then
write (nu_diag, *) 'tracer index depend type has_dependents'
write (nu_diag, *) 'tracer index depend type has_dependents'
nt = 1
write(nu_diag,*) ' hi ',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'hi ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
nt = 2
write(nu_diag,*) ' hs ',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'hs ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
k=2
do nt = k+1, k+ntrcr
if (nt-k==nt_Tsfc) &
write(nu_diag,*) 'nt_Tsfc',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_Tsfc ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_qice) &
write(nu_diag,*) 'nt_qice',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_qice ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_qsno) &
write(nu_diag,*) 'nt_qsno',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_qsno ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_sice) &
write(nu_diag,*) 'nt_sice',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_sice ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_fbri) &
write(nu_diag,*) 'nt_fbri',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_fbri ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_iage) &
write(nu_diag,*) 'nt_iage',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_iage ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_FY) &
write(nu_diag,*) 'nt_FY ', nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_FY ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_alvl) &
write(nu_diag,*) 'nt_alvl',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_alvl ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_vlvl) &
write(nu_diag,*) 'nt_vlvl',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_vlvl ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_apnd) &
write(nu_diag,*) 'nt_apnd',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_apnd ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_hpnd) &
write(nu_diag,*) 'nt_hpnd',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_hpnd ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_ipnd) &
write(nu_diag,*) 'nt_ipnd',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_ipnd ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_fsd) &
write(nu_diag,*) 'nt_fsd ',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_fsd ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_isosno) &
write(nu_diag,*) 'nt_isosno',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_isosno ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_isoice) &
write(nu_diag,*) 'nt_isoice',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_isoice ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_bgc_Nit) &
write(nu_diag,*) 'nt_bgc_Nit',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_bgc_Nit ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
if (nt-k==nt_bgc_S) &
write(nu_diag,*) 'nt_bgc_S',nt,depend(nt),tracer_type(nt),&
write(nu_diag,1000) 'nt_bgc_S ',nt,depend(nt),tracer_type(nt),&
has_dependents(nt)
enddo
write(nu_diag,*) ' '
endif ! master_task
1000 format (1x,a,2x,i6,2x,i6,2x,i4,4x,l4)

if (trim(advection)=='remap') call init_remap ! grid quantities

Expand Down
16 changes: 10 additions & 6 deletions cicecore/cicedynB/general/ice_init.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ subroutine input_data
runid, runtype, use_restart_time, restart_format, lcdf64
use ice_history_shared, only: hist_avg, history_dir, history_file, &
incond_dir, incond_file, version_name, &
history_precision
history_precision, history_format
use ice_flux, only: update_ocn_f, l_mpond_fresh
use ice_flux, only: default_season
use ice_flux_bgc, only: cpl_bgc
Expand Down Expand Up @@ -150,7 +150,7 @@ subroutine input_data
ice_ic, restart, restart_dir, restart_file, &
restart_ext, use_restart_time, restart_format, lcdf64, &
pointer_file, dumpfreq, dumpfreq_n, dump_last, &
diagfreq, diag_type, diag_file, &
diagfreq, diag_type, diag_file, history_format,&
print_global, print_points, latpnt, lonpnt, &
dbug, histfreq, histfreq_n, hist_avg, &
history_dir, history_file, history_precision, cpl_bgc, &
Expand Down Expand Up @@ -250,6 +250,7 @@ subroutine input_data
histfreq(5) = 'y' ! output frequency option for different streams
histfreq_n(:) = 1 ! output frequency
hist_avg = .true. ! if true, write time-averages (not snapshots)
history_format = 'default' ! history file format
history_dir = './' ! write to executable dir for default
history_file = 'iceh' ! history file name prefix
history_precision = 4 ! precision of history files
Expand All @@ -264,9 +265,9 @@ subroutine input_data
restart_dir = './' ! write to executable dir for default
restart_file = 'iced' ! restart file name prefix
restart_ext = .false. ! if true, read/write ghost cells
use_restart_time = .true. ! if true, use time info written in file
use_restart_time = .true. ! if true, use time info written in file
pointer_file = 'ice.restart_file'
restart_format = 'nc' ! file format ('bin'=binary or 'nc'=netcdf or 'pio')
restart_format = 'default' ! restart file format
lcdf64 = .false. ! 64 bit offset for netCDF
ice_ic = 'default' ! latitude and sst-dependent
grid_format = 'bin' ! file format ('bin'=binary or 'nc'=netcdf)
Expand Down Expand Up @@ -539,6 +540,7 @@ subroutine input_data
call broadcast_scalar(history_dir, master_task)
call broadcast_scalar(history_file, master_task)
call broadcast_scalar(history_precision, master_task)
call broadcast_scalar(history_format, master_task)
call broadcast_scalar(write_ic, master_task)
call broadcast_scalar(cpl_bgc, master_task)
call broadcast_scalar(incond_dir, master_task)
Expand Down Expand Up @@ -1002,6 +1004,8 @@ subroutine input_data
write(nu_diag,*) ' history_file = ', &
trim(history_file)
write(nu_diag,1020) ' history_precision = ', history_precision
write(nu_diag,*) ' history_format = ', &
trim(history_format)
if (write_ic) then
write(nu_diag,*) 'Initial condition will be written in ', &
trim(incond_dir)
Expand Down Expand Up @@ -1165,8 +1169,8 @@ subroutine input_data
oceanmixed_ice
write(nu_diag,1010) ' wave_spec = ', wave_spec
if (wave_spec) then
write(nu_diag,*) ' wave_spec_type = ', wave_spec_type
write(nu_diag,*) ' wave_spec_file = ', wave_spec_file
write(nu_diag,*) ' wave_spec_type = ', trim(wave_spec_type)
write(nu_diag,*) ' wave_spec_file = ', trim(wave_spec_file)
endif
write(nu_diag,1020) ' nfreq = ', nfreq
write(nu_diag,*) ' tfrz_option = ', &
Expand Down
2 changes: 1 addition & 1 deletion cicecore/cicedynB/infrastructure/ice_grid.F90
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Expand Up @@ -2411,7 +2411,7 @@ subroutine get_bathymetry_popfile
! create thickness profile
k1 = min(5,nlevel)
do k = 1,k1
thick(k) = max(10000._dbl_kind/float(nlevel),500.)
thick(k) = max(10000._dbl_kind/float(nlevel),500._dbl_kind)
enddo
do k = k1+1,nlevel
thick(k) = min(thick(k-1)*1.2_dbl_kind,20000._dbl_kind)
Expand Down
2 changes: 1 addition & 1 deletion cicecore/cicedynB/infrastructure/ice_restart_driver.F90
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Expand Up @@ -883,7 +883,7 @@ subroutine restartfile_v4 (ice_ic)
if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
file=__FILE__, line=__LINE__)

! creates netcdf if restart_format = 'nc'
! creates new file
filename = trim(restart_dir) // '/iced.converted'
call dumpfile(filename)
call final_restart
Expand Down
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